Fix: PFB manifest generator uses server-side paging (#7872) by nadove-ucsc · Pull Request #7873 · DataBiosphere/azul

nadove-ucsc · 2026-03-17T02:24:10Z

Linked issues: #7872

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coveralls · 2026-03-17T02:36:52Z

coverage: 85.064% (+0.005%) from 85.059%
when pulling a3660c8 on issues/nadove-ucsc/7872-pfb-manifest-server-side-paging
into dc72fb4 on develop.

src/azul/service/manifest_service.py

codecov · 2026-03-17T04:03:31Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.92%. Comparing base (3aecff8) to head (a3660c8).
⚠️ Report is 5 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #7873   +/-   ##
========================================
  Coverage    84.91%   84.92%           
========================================
  Files          161      161           
  Lines        23104    23106    +2     
========================================
+ Hits         19619    19622    +3     
+ Misses        3485     3484    -1

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nadove-ucsc · 2026-03-17T20:48:54Z

Note that while many of these changes were previously reviewed as part of #7775, there have been several changes made since then.

achave11-ucsc

Are the fixup! commits intended for something in particular?

achave11-ucsc · 2026-03-18T03:20:08Z

src/azul/service/manifest_service.py

+                       request_factory: Callable[[SortKey | None], Search]
+                       ) -> Iterable[Hit]:
+        """
+        Yield all hits in every page of Opensearch hits in responses to


Suggested change

Yield all hits in every page of Opensearch hits in responses to

Yield all hits in every page of OpenSearch hits in responses to

achave11-ucsc · 2026-03-18T03:24:41Z

src/azul/service/manifest_service.py

+        Yield all hits in every page of Opensearch hits in responses to
+        requests that use client-side paging.
+
+        :param request_factory:  A callable that returns a prepared Opensearch


Suggested change

:param request_factory: A callable that returns a prepared Opensearch

:param request_factory: A callable that returns a prepared OpenSearch

achave11-ucsc · 2026-03-18T03:32:39Z

src/azul/service/manifest_service.py

-                return request.extra(search_after=search_after)
-
-        return self._paginate_hits(request_factory)
+        sort = ('entity_id.keyword', '_id')


Suggested change

sort = ('entity_id.keyword', '_id')

sort = ['entity_id.keyword', '_id']

For consistency with the usage above.

hits = self._paginate_hits_sorted(request, sort=['entity_id.keyword'])

achave11-ucsc · 2026-03-18T03:38:12Z

src/azul/service/manifest_service.py

    IO,
    Protocol,
    Self,
+    Sequence,


Deprecated, consider using collections.abc.Sequence instead.

This facilitates the upcoming switch to client-side paging in PFBManifestGenerator, where only a single field is used for sorting.

nadove-ucsc · 2026-03-18T22:46:39Z

Are the fixup! commits intended for something in particular?

They were originally made in response to @hannes-ucsc 's feedback on the PR this was split off from, but I've now squashed them.

Eliminating the call to `scan` helps facilitate the transition to template queries

achave11-ucsc

Approved ✅

hannes-ucsc · 2026-03-19T16:59:57Z

src/azul/service/query_service.py



-type SortKey = tuple[PrimitiveJSON, str]
+type SortKey = tuple[PrimitiveJSON, ...]


I don't think we want to remove the size constraint.

Agreed at PL to try using a type union to accommodate both the 1-element case and the 2-element while keeping the type as narrow as possible.

nadove-ucsc self-assigned this Mar 17, 2026

nadove-ucsc linked an issue Mar 17, 2026 that may be closed by this pull request

PFB manifest generator uses server-side paging #7872

Open

nadove-ucsc force-pushed the issues/nadove-ucsc/7872-pfb-manifest-server-side-paging branch from cf905e1 to d0c6952 Compare March 17, 2026 03:08

github-advanced-security bot found potential problems Mar 17, 2026

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src/azul/service/manifest_service.py Fixed Show fixed Hide fixed

nadove-ucsc force-pushed the issues/nadove-ucsc/7872-pfb-manifest-server-side-paging branch from 4a6789a to 2f4a768 Compare March 17, 2026 03:39

nadove-ucsc requested a review from achave11-ucsc March 17, 2026 20:47

nadove-ucsc assigned achave11-ucsc Mar 17, 2026

achave11-ucsc requested changes Mar 18, 2026

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achave11-ucsc removed their assignment Mar 18, 2026

nadove-ucsc added 4 commits March 18, 2026 11:17

Remove unused function

98a1108

Use JSON narrowing function

42911c5

Widen SortKey type alias

88e1fb6

This facilitates the upcoming switch to client-side paging in PFBManifestGenerator, where only a single field is used for sorting.

Pull up method

e6b5962

nadove-ucsc added 4 commits March 18, 2026 15:49

fixup! Pull up method

e5577fa

Extract method

6bfdbc7

fixup! Extract method

fea5f95

Legacy PFB manifest uses client-side paging

a3660c8

Eliminating the call to `scan` helps facilitate the transition to template queries

nadove-ucsc force-pushed the issues/nadove-ucsc/7872-pfb-manifest-server-side-paging branch from 600cdcd to e5577fa Compare March 18, 2026 22:53

nadove-ucsc requested a review from achave11-ucsc March 19, 2026 00:48

nadove-ucsc assigned achave11-ucsc Mar 19, 2026

achave11-ucsc approved these changes Mar 19, 2026

View reviewed changes

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Mar 19, 2026

achave11-ucsc marked this pull request as ready for review March 19, 2026 04:39

achave11-ucsc requested a review from hannes-ucsc as a code owner March 19, 2026 04:39

hannes-ucsc requested changes Mar 19, 2026

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hannes-ucsc removed their assignment Mar 19, 2026

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Fix: PFB manifest generator uses server-side paging (#7872)#7873

Fix: PFB manifest generator uses server-side paging (#7872)#7873
nadove-ucsc wants to merge 8 commits intodevelopfrom
issues/nadove-ucsc/7872-pfb-manifest-server-side-paging

nadove-ucsc commented Mar 17, 2026 •

edited by achave11-ucsc

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	Yield all hits in every page of Opensearch hits in responses to
	Yield all hits in every page of OpenSearch hits in responses to

	:param request_factory: A callable that returns a prepared Opensearch
	:param request_factory: A callable that returns a prepared OpenSearch

	sort = ('entity_id.keyword', '_id')
	sort = ['entity_id.keyword', '_id']



		type SortKey = tuple[PrimitiveJSON, str]
		type SortKey = tuple[PrimitiveJSON, ...]

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nadove-ucsc commented Mar 17, 2026 •

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